ctrl+shift+p filters: :st2 :st3 :win :osx :linux
Browse

nextflow

by peterk87 ST3

Nextflow workflow syntax highlighting and snippets for Sublime Text 3

Labels language syntax, snippets, completions

Details

Installs

  • Total 0
  • Win 0
  • OS X 0
  • Linux 0
Dec 7 Dec 6 Dec 5 Dec 4 Dec 3 Dec 2 Dec 1 Nov 30 Nov 29 Nov 28 Nov 27 Nov 26 Nov 25 Nov 24 Nov 23 Nov 22 Nov 21 Nov 20 Nov 19 Nov 18 Nov 17 Nov 16 Nov 15 Nov 14 Nov 13 Nov 12 Nov 11 Nov 10 Nov 9 Nov 8 Nov 7 Nov 6 Nov 5 Nov 4 Nov 3 Nov 2 Nov 1 Oct 31 Oct 30 Oct 29 Oct 28 Oct 27 Oct 26 Oct 25 Oct 24
Windows 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
OS X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Linux 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Readme

Source
raw.​githubusercontent.​com

sublime-nextflow: Nextflow workflow syntax highlighting and snippets for Sublime Text 3

[Insert pretty screenshot here]()

Nextflow Syntax Highlighting

Nextflow syntax highlighting extends Sublime Text 3's Groovy syntax with highlighting of:

  • processes
    • input/output/script tags
  • channel highlighting based on matching ch_*
  • some invalid syntax checks (into channel in input tag and from channel in output tag)
  • highlighting special Nextflow functions and variables (workflow, params, task, etc)

Nextflow Snippets

  • proc: process snippet
  • tag: tag directive snippet
  • pub: publishDir directive snippet
  • init: initialize a Nextflow workflow (shebang, some initial params and a help message)
  • illumina: Illumina paired-end reads file pairs channel
  • par: Create a new params parameter (params.<param_name> = <default>)
  • cpus: insert “${task.cpus}” into a script
  • script_path: specify user script (e.g. Python script) to use from scripts/ directory in workflow base directory
  • info: log.info snippet
  • done: on workflow complete or error message